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For any general information about the application, support, or to report a bug, contact Application Support. |
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Download each of the tools listed in the bulleted list above and follow the installation instructions provided with each respective product for your environment. Assistance from a MySQL database administrator is expected to properly configure the MySQL database. For MySQL database configuration and maintenance, it is also helpful to download the MySQL workbench (suite of GUI tools) at http://www.mysql.com/downloads/workbench/
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Obtaining the caNanoLab Source
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The caNanoLab source distribution caNanoLab_2.0.zip is downloaded. Ant is installed.
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Step 1. Extract caNanoLab
Extract the the caNanoLab_2.0.zip to a location on your local system, for example, C:\caNanoLab_2.0. This location is referred to as <CANANOLAB_SOURCE> throughout the document. Verify that the following five folders exist in the directory <CANANOLAB_SOURCE>:
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Assumptions and Requirements
- The Ant build properties are set as described in in section, Step 2. Edit Ant Properties.
- A MySQL database is set up on a system (local or remote) with a system (or root) account.
- The system account matches properties 9) and properties 10) in Step 2. Edit Ant Properties.
For a Previous Installation
If you installed caNanoLab prior to release 2.0 against 0 against an MySQL database, or release 1.2, release 1.1.1, or release 1.1 against an Oracle database, and have associated production data in these schemas and you would like to continue to use the same data for caNanoLab release 2.0 in MySQL, review the following database initialization steps, and then go directly to section, Data Migration.
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This installation guide only discusses the steps for migrating from release 1.5.3, 1.5.4, or 1.5.5. in MySQL MySQL to release 2.0 in MySQL. If you have previously installed caNanoLab in MySQL prior to release 1.5.1, you need to migrate to release 1.5.1 first, one release at a time. The 1.5.5 installation guide is available at the main caNanoLab wiki page, but previous installation guides are available at the caNanoLab Archive page.
Follow these steps to complete the required data migration from release 1.5.3, 1.5.4, or 1.5.5. in MySQL to release 2.0 in MySQL:
Step | Action |
1 | Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target update:cananolab-db. Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script updates the database schema and seed data required the caNanoLab 2.0 release. |
2 | If you are NOT using LDAP for user authentication, you can skip this step. If you are using LDAP for authentication, execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target update:cananolab-db:ldap:upt:superadmin Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file. |
3 | If you are NOT using LDAP for user authentication, you can skip this step. If you are using LDAP for authentication, and you already have user accounts in the system and you have data created by these users whose login names are not their LDAP login IDs, you need to perform the following update:
Note: if the created_by field contains the word "COPY" in it, update it with a prefix : (colon), where the token is replaced by the real LDAP login name that corresponds to the old login name who created the data. If you do not know the original login who created the data, use the LDAP login of a curator. If you need assistance on completing the data updates for this step, please contact the caNanoLab technical team. |
After data migration, refer to the Verification section to verify that the migration is successful.
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Step | Action | ||
1 | Set up an environment variable JBOSS_HOME to point to the JBoss installation directory. | ||
2 | Execute the Ant build script build.xml located at Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script generates the following artifacts that include two deployable web archive war files, configuration files and libraries for running the web application in the JBoss environment, and also places these artifacts in the appropriate directories under <JBOSS_HOME>:
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3 | We recommend increasing the JBoss JVM heap size to 1G bytes and permanent generation (permgen) memory space to 256M bytes by updating the file
This configuration file is read when JBoss server starts. | ||
4 | When deploying the caNanolab application in a production environment, we also recommend updating the default logging behavior of the JBoss server by turning off the unnecessary loggings thus reducing file system requirements for server log files.
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Verification
Once the deployment artifacts are deployed and the JBoss application server is correctly configured, you can now start the JBoss application server, which in turn starts the caNanoLab application.
Open the URL http://<APP_SERVER_URL>/caNanoLab/
, for example, http://localhost:8080/caNanoLab
). The Welcome/Login page displays.
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Step | Action |
1 | Launch the UPT tool at http://<APP_SERVER_URL>/uptlogin and log in as the super admin. If you are NOT using LDAP for user authentication, the default user account/password for super admin is superadmin/superadmin . Enter csmupt as the application name when prompted at the UPT log in. If you are using LDAP for user authentication, use the LDAP login name and password of the user assigned as the super admin as specified in the Ant build properties file. |
2 | If you are using LDAP for user authentication, skip this step. If you are not using LDAP for authentication, follow this step to reset the password for superadmin :
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3 | Log in as the super admin, and follow these steps to create a new user and assign it to be a caNanoLab administrator:
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4 | Before the newly-created user can log into the UPT application, logged in as the super admin, follow these steps to update the required database connection information for the csmupt and caNanoLab applications under the Application tab: Select Application > Select an Existing Application, and click Search. Select csmupt from the application list. Click View Details, then update the following fields:
Note: Please refer to Edit Ant Properties for the appropriate values for these fields. Values for Application Database Dialect and Application Database Driver must be exactly entered as shown above. Repeat the steps to update the database connection information for the caNanoLab application. |
5 | Log out of the UPT tool and log back in as admin. Use caNanoLab as the application name when prompted at the UPT log in. |
6 | Select User > Select an Existing User, and click Search. Select admin from the User list. Click View Details, then Associated Groups. Select Curator from the pre-defined group list and assign it to the user. Click Update Associations to commit the change. |
Follow similar steps to create other application user accounts as appropriate.
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For more information about how to use the UPT tool for managing user accounts, contact NCI CBIIT Application Support at nciappsupport@nih.gov and request that the caNanoLab technical team gives you a demonstration of the UPT tool in the context of the caNanoLab application.
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